For starters, you should locate the data file for the tempdb on your fastest disk, and separate the windchill database data and transaction log files to separate disks for better I/O. Unfortunately the PSI and SCUputs these latter two in one directory with no option to relocate during initial installation, so you'll need to move them afterwards using scripts (see http://support.microsoft.com/kb/224071).
The tempdb is very important for performance, and it is recreated every time you restart the server. You should set the initial size of the tempdb to match whatever size it grows to after your Windchill server has been running for a few days.
EDC group at PTC isworking on a document onSQL Server w/Windchillinitial planning and installation that should be available soon, and Microsoft is also working on a best practices document for SQL Server w/Windchill.